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- PDB-8z1v: Cryo-EM structure of Escherichia coli DppBCDF in the resting state -

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Basic information

Entry
Database: PDB / ID: 8z1v
TitleCryo-EM structure of Escherichia coli DppBCDF in the resting state
Components
  • Dipeptide transport ATP-binding protein DppD
  • Dipeptide transport ATP-binding protein DppF
  • Dipeptide transport system permease protein DppB
  • Dipeptide transport system permease protein DppC
KeywordsTRANSPORT PROTEIN / ABC importer / Complex / Peptide transporter
Function / homology
Function and homology information


ABC-type dipeptide transporter / dipeptide transport / dipeptide transmembrane transporter activity / heme transmembrane transporter activity / heme transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to radiation / protein transport / 4 iron, 4 sulfur cluster binding / ATP hydrolysis activity ...ABC-type dipeptide transporter / dipeptide transport / dipeptide transmembrane transporter activity / heme transmembrane transporter activity / heme transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to radiation / protein transport / 4 iron, 4 sulfur cluster binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
: / : / Oligopeptide transport permease C-like, N-terminal domain / N-terminal TM domain of oligopeptide transport permease C / ABC transporter type 1, GsiC-like, N-terminal domain / : / : / Binding-prot-dependent transport system membrane comp, N-term / Oligopeptide/dipeptide ABC transporter, C-terminal / Oligopeptide/dipeptide transporter, C-terminal region ...: / : / Oligopeptide transport permease C-like, N-terminal domain / N-terminal TM domain of oligopeptide transport permease C / ABC transporter type 1, GsiC-like, N-terminal domain / : / : / Binding-prot-dependent transport system membrane comp, N-term / Oligopeptide/dipeptide ABC transporter, C-terminal / Oligopeptide/dipeptide transporter, C-terminal region / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Dipeptide transport ATP-binding protein DppD / Dipeptide transport system permease protein DppB / Dipeptide transport system permease protein DppC / Dipeptide transport ATP-binding protein DppF
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsLi, P. / Huang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: PLoS Biol / Year: 2025
Title: Structural characterization of the ABC transporter DppABCDF in Escherichia coli reveals insights into dipeptide acquisition.
Authors: Panpan Li / Manfeng Zhang / Yihua Huang /
Abstract: The prokaryote-specific ATP-binding cassette (ABC) peptide transporters are involved in various physiological processes and plays an important role in transporting naturally occurring antibiotics ...The prokaryote-specific ATP-binding cassette (ABC) peptide transporters are involved in various physiological processes and plays an important role in transporting naturally occurring antibiotics across the membrane to their intracellular targets. The dipeptide transporter DppABCDF in Gram-negative bacteria is composed of five distinct subunits, yet its assembly and underlying peptide import mechanism remain elusive. Here, we report the cryo-EM structures of the DppBCDF translocator from Escherichia coli in both its apo form and in complexes bound to nonhydrolyzable or slowly hydrolyzable ATP analogs (AMPPNP and ATPγS), as well as the ATPγS-bound DppABCDF full transporter. Unlike the reported heterotrimeric Mycobacterium tuberculosis DppBCD translocator, the E. coli DppBCDF translocator is a heterotetramer, with a [4Fe-4S] cluster at the C-terminus of each ATPase subunit. Structural studies reveal that ATPγS/AMPPNP-bound DppBCDF adopts an inward-facing conformation, similar to that of apo-DppBCDF, with only one ATPγS or AMPPNP molecule bound to DppF. By contrast, ATPγS-bound DppABCDF adopts an outward-facing conformation, with two ATPγS molecules glueing DppD and DppF at the interface. Consistent with structural observations, ATPase activity assays show that the DppBCDF translocator itself is inactive and its activation requires concurrent binding of DppA and ATP. In addition, bacterial complementation experiments imply that a unique periplasmic scoop motif in DppB may play important roles in ensuring dipeptide substrates import across the membrane, presumably by preventing dipeptide back-and-forth binding to DppA and avoiding dipeptides escaping into the periplasm upon being released from DppA.
History
DepositionApr 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Dipeptide transport system permease protein DppB
B: Dipeptide transport system permease protein DppC
C: Dipeptide transport ATP-binding protein DppD
D: Dipeptide transport ATP-binding protein DppF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,0626
Polymers143,3594
Non-polymers7032
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Dipeptide transport system permease protein DppB


Mass: 37531.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dppB, b3543, JW3512 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEF8
#2: Protein Dipeptide transport system permease protein DppC


Mass: 32328.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dppC, b3542, JW3511 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEG1
#3: Protein Dipeptide transport ATP-binding protein DppD


Mass: 35887.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dppD, b3541, JW3510 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AAG0, ABC-type dipeptide transporter
#4: Protein Dipeptide transport ATP-binding protein DppF


Mass: 37611.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dppF, dppE, b3540, JW3509 / Production host: Escherichia coli (E. coli) / References: UniProt: P37313, ABC-type dipeptide transporter
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DppBCDF / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.143 MDa / Experimental value: YES
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 411381 / Symmetry type: POINT

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